reverted merge

.gitignore

@@ -1,4 +1,10 @@
 
+*.o
+
+doc/*
+
+debug_amici/*
+
 models/*
 
 doc/*
@@ -17,7 +23,7 @@ images/*
 
 *.mexmaci64
 
-*.o
+*.eps
 
 *.js
 
@@ -61,24 +67,28 @@ examples/example_6/html/*
 
 *.mat
 
+mtoc/makeExampleDoc.m
+
+mtoc/makeDocumentation.m
+
 examples/example_5/example_model_5_paper.m
 
-*.m~
+mtoc/makeDocumentation.m
 
-*.plist
+mtoc/makeDocumentation.m
 
-*.pbxproj
+index.html
 
-*.xcworkspacedata
+*.js
 
-*.xcuserstate
+*.template
 
-*.xcsettings
+*.dox
 
-*.xcbkptlist
+*.json
 
-*.xcscheme
+examples/geneExpression/simulate_geneExpression.m
 
-*.xccheckout
+*.m~
 
 *.plist

@SBMLode/SBMLode.m

@@ -1,71 +1,38 @@
-%
-% @file amioption
-% @brief definition of amioption class
-%
 classdef SBMLode < handle
-    %SBMLODE carries all information about the differential equation
-    %defined by a SBML model definition file. This class acts as an
-    %interface between SBML files and \ref amimodel
+    %SBMLMODEL Summary of this class goes here
+    %   Detailed explanation goes here
 
     properties
-        % vector of non-constant and non-boundary states @type symbolic
-        state = sym([]);
-        % vector of guessed observables @type symbolic
-        observable = sym([]);
-        % vector of guessed observable names @type symbolic
-        observable_name = sym([]);
-        % vector of SBML parameters @type symbolic
-        param = sym([]);
-        % vector of amimodel parameters @type symbolic
-        parameter = sym([]);
-        % vector of constant states @type symbolic
-        constant = sym([]);
-        % vector of compartments @type symbolic
-        compartment = sym([]);
-        % vector of compartment volumes @type symbolic
-        volume = sym([]);
-        % vector of initial values for non-constant and non-boundary states @type symbolic
-        initState = sym([]);
-        % vector of boundary condition states which are not constant @type symbolic
-        condition = sym([]);
-        % vector of reaction fluxes @type symbolic
-        flux = sym([]);
-        % matrix of reaction stochiometries @type symbolic
-        stochiometry = sym([]);
-        % right hand side of differential equation for states @type symbolic
-        xdot = sym([]);
-        % vector of trigger functions for events @type symbolic
-        trigger = sym([]);
-        % matrix of event bolus @type symbolic
-        bolus = sym([]);
-        % cell array containing the function definition @type cell
-        funmath = {};
-        % cell array containing the function arguments @type cell
-        funarg = {};
-        % expression for time in the model @type char
-        time_symbol = char([]);
-        % nominal parameter value @type sym
-        pnom = double([]);
-        % nominal condition value @type sym
-        knom = double([]);
+        state@sym;
+        observable@sym;
+        observable_name@sym;
+        param@sym;
+        parameter@sym;
+        constant@sym;
+        reaction@sym;
+        compartment@sym;
+        volume@sym;
+        initState@sym;
+        condition@sym;
+        flux@sym;
+        stochiometry@sym;
+        xdot@sym;
+        trigger@sym;
+        bolus@sym;
+        funmath@cell;
+        funarg@cell;
+        time_symbol@char;
+        pnom@double;
+        knom@double;
     end
 
     methods
         function model = SBMLode(filename)
-            % constructor of the SBMLode class. This takes the name of an
-            % SBML definition file and constructs an SBMLode object based
-            % on the parsed model
-            % 
-            % Parameters:
-            %  filename: SBML definition file @type char
-            %
-            % Return values:
-            %  out: optimized expression @type SBMLode
             model.importSBML(filename);
         end
 
-        importSBML(this,filename)
 
+        importSBML(this,filename)
         writeAMICI(this,modelname)
     end
 

@SBMLode/importSBML.m

@@ -1,13 +1,4 @@
 function importSBML(this,modelname)
-    % importSBML parses the SBML document and initialises the respective
-    % \ref SBMLode object accordingly
-    %
-    % Parameters:
-    %  modelname: name of the sbml model file, without extension
-    %
-    % Return values:
-    %  this: initialised SBMLode object object @type SBMLode
-
     try
         model = TranslateSBML([modelname '.sbml']);
     catch

@SBMLode/writeAMICI.m

@@ -1,13 +1,4 @@
 function writeAMICI(this,modelname)
-    % importSBML writes the information stored in the SBMLode object into
-    % an AMICI model definition file
-    %
-    % Parameters:
-    %  modelname: target name of the AMICI model definition file, _syms
-    %  will be appended
-    %
-    % Return values:
-    %  this: initialised SBMLode object object @type SBMLode
     fprintf('writing file ...\n')
     fid = fopen([modelname '_syms.m'],'w');
 

@amidata/amidata.m

@@ -18,17 +18,17 @@
         % number of conditions/constants
         nk=0;
         % timepoints of observations
-        t = double([]);
+        t@double;
         % observations
-        Y = double([]);
+        Y@double;
         % standard deviation of observations
-        Sigma_Y = double([]);
+        Sigma_Y@double;
         % event observations
-        Z = double([]);
+        Z@double;
         % standard deviation of event observations
-        Sigma_Z = double([]);
+        Sigma_Z@double;
         % experimental condition
-        condition = double([]);
+        condition@double
     end
 
     methods

@amievent/amievent.m

@@ -8,32 +8,18 @@
 
     properties ( GetAccess = 'public', SetAccess = 'private' )
         % the trigger function activates the event on every zero crossing @type symbolic
-        trigger = sym([]);
+        trigger@sym;
         % the bolus function defines the change in states that is applied on every event occurence @type symbolic
-        bolus = sym([]);
+        bolus@sym;
         % output function for the event @type symbolic
-        z = sym([]);
+        z@sym;
         % flag indicating that a heaviside function is present, this helps
-        % to speed up symbolic computations @type logical
-        hflag = logical([]);
+        % to speed up symbolic computations
+        hflag@logical;
     end
 
     methods
         function AE = amievent(trigger,bolus,z)
-            % constructor of the amievent class. this function constructs an event object based on the provided
-            % trigger function, bolus function and output function
-            %
-            % Parameters:
-            %  trigger: trigger fuction, the roots of this function define
-            %  the occurence of the event @type symbolic
-            %  bolus: bolus fuction, this function defines the change in 
-            %  the states on event occurences @type symbolic
-            %  z: output function, this expression is evaluated on event
-            %  occurences and returned by the simulation function @type
-            %  symbolic
-            % 
-            % Return values:
-            %  AM: model definition object
             if(~isa(trigger,'sym'))
                 if(isa(trigger,'double'))
                     AE.trigger = sym(trigger);

@amievent/setHflag.m

@@ -2,7 +2,7 @@
     % gethflag sets the hflag property.
     %
     % Parameters:
-    %  hflag: value for the hflag property @type double
+    %  hlfag: value for the hflag property @type double
     %
     % Return values:
     %  this: updated event definition object @type amievent

@amifun/amifun.m

@@ -8,39 +8,30 @@
 
     properties ( GetAccess = 'public', SetAccess = 'public' )
         % symbolic definition struct @type symbolic
-        sym;
+        sym@sym;
         % short symbolic string which can be used for the reuse of precomputed values @type symbolic
-        strsym;
+        strsym@sym;
         % short symbolic string which can be used for the reuse of old values @type symbolic
-        strsym_old;
+        strsym_old@sym;
         % name of the model @type char
-        funstr;
+        funstr@char;
         % name of the c variable @type char
-        cvar;
+        cvar@char;
         % argument string (solver specific) @type char
-        argstr;
+        argstr@char;
         % argument string (solver unspecific) @type char
-        fargstr;
+        fargstr@char;
         % dependencies on other functions @type cell
-        deps;
-        % nvec dependencies @type cell
-        nvecs;
+        deps@cell;
+        % nvec dependencies
+        nvecs@cell;
         % indicates whether the function is a sensitivity or derivative
-        % with respect to parameters @type logical
-        sensiflag;
+        % with respect to parameters
+        sensiflag@logical;
     end
 
     methods
         function AF = amifun(funstr,model)
-            % constructor of the amifun class. this function initializes the function object based on the provided
-            % function name funstr and model definition object model
-            %
-            % Parameters:
-            %  funstr: name of the function @type string
-            %  model: model definition object @type amimodel
-            % 
-            % Return values:
-            %  AM: model definition object
             AF.funstr = funstr;
             AF = AF.getDeps(model);
             AF = AF.getArgs(model);
@@ -49,7 +40,7 @@
             AF = AF.getCVar();
             AF = AF.getSensiFlag();
         end
-        
+
         printLocalVars(this,model,fid)
 
         writeCcode_sensi(this,model,fid)
@@ -62,15 +53,13 @@
 
         [ this ] = getArgs(this,model)
 
-        [ this ] = getFArgs(this,model)
-
         [ this ] = getNVecs(this)
 
         [ this ] = getCVar(this)
 
-        [ this ] = getSyms(this,model)
-
         [ this ] = getSensiFlag(this)
+
+        [ this ] = checkDeps(this)
     end
 end